MolNFT v1 · #53956 · protein
Crystal structure of deacetylase-teicoplanin complex in biosynthesis pathway of teicoplanin
2XAD · N-acyl glm peudo-teicoplanin deacetylase: “Crystal structure of deacetylase-teicoplanin complex in biosynthesis pathway of teicoplanin”. X-ray diffraction, 4 ligands (T55, BMA, NAG), 15 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 2XAD
- Type
- protein
- Length
- 1,058 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acyl glm peudo-teicoplanin deacetylase; Teicoplanin
- UniProt
- Q6ZZJ1
- Ligands
- T55, BMA, NAG, GCS
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acyl glm peudo-teicoplanin deacetylase | protein | 259 | 43% helix, 19% strand | Q6ZZJ1 |
| B | N-acyl glm peudo-teicoplanin deacetylase | protein | 257 | 43% helix, 18% strand | Q6ZZJ1 |
| C | N-acyl glm peudo-teicoplanin deacetylase | protein | 257 | 42% helix, 19% strand | Q6ZZJ1 |
| D | N-acyl glm peudo-teicoplanin deacetylase | protein | 257 | 43% helix, 19% strand | Q6ZZJ1 |
| E, F, G, H | Teicoplanin | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- T55 · 8-methylnonanoic acid · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains E, A, F, G, D, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, E, B, F, C, G, D, H
- GCS · 2-amino-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.85 | 0.86 | 111 | empty |
| 2 | 323 | 0.76 | 0.87 | 34 | NAG, GCS, T55 |
| 3 | 231 | 0.73 | 0.88 | 32 | NAG, GCS, T55 |
| 4 | 285 | 0.71 | 0.85 | 30 | GCS, T55 |
| 5 | 310 | 0.71 | 0.84 | 50 | empty |
Interfaces
11 interfaces between chains.
- B–F · 627 Ų buried · 6 hydrogen bonds · protein-protein
- D–H · 610 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 562 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 538 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 500 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified, 12 glycan (nonstandard, glycosylation, engineered).
Compared structures
- 2XAD · Crystal structure of deacetylase-teicoplanin complex in biosynthesis pathway of… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q6ZZJ1
- Elsewhere: RCSB PDB 2XAD · PDBe 2XAD · UniProt Q6ZZJ1
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